Strain identifier

BacDive ID: 17005

Type strain: Yes

Species: Actinomadura geliboluensis

Strain Designation: A8036

Strain history: <- Nevzat Sahin, Ondokuz Mayis Univ., Turkey

NCBI tax ID(s): 882440 (species)

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General

@ref: 17455

BacDive-ID: 17005

DSM-Number: 45508

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive

description: Actinomadura geliboluensis A8036 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 882440
  • Matching level: species

strain history

@refhistory
17455<- N. Sahin, Ondokuz Mayis Univ., Dept. of Biology, Kurupelit-Samsun, Turkey; A8036
67770KCTC 19868 <-- N. Sahin A8036.
67771<- Nevzat Sahin, Ondokuz Mayis Univ., Turkey

doi: 10.13145/bacdive17005.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Thermomonosporaceae
  • genus: Actinomadura
  • species: Actinomadura geliboluensis
  • full scientific name: Actinomadura geliboluensis Sazak et al. 2012

@ref: 17455

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura geliboluensis

full scientific name: Actinomadura geliboluensis Sazak et al. 2012

strain designation: A8036

type strain: yes

Morphology

cell morphology

@refgram stainmotility
30440positiveno
67771positive

colony morphology

@refcolony colormedium used
69400Ivory (1014)ISP 2
69400Ivory (1014)ISP 4
69400Ivory (1014)ISP 5
69400Ivory (1014), light ivory (1015)ISP 7
69400Sand yellow (1002)ISP 6
69400Sand yellow (1002), grey beige (1019)suter with tyrosine
69400Yellow grey (7034)suter without tyrosine

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
69400yesAerial myceliumSignal white (9003)ISP 2
69400yesAerial myceliumPure white (9010)ISP 3
69400yesAerial myceliumTraffic white (9016)ISP 4
69400noAerial myceliumISP 5
69400noAerial myceliumISP 6
69400noAerial myceliumISP 7
69400yesAerial myceliumsuter with tyrosine
69400noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
30440no
69400nosoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
69400DSM_45508_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69400DSM_45508_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17455TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
17455GPHF-MEDIUM (DSMZ Medium 553)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf
17455GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
17455positivegrowth28mesophilic
30440positivegrowth20-45
30440positiveoptimum30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30440positivegrowth05-11alkaliphile
30440positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30440aerobe
67771aerobe

spore formation

  • @ref: 30440
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
30440NaClpositivegrowth0-5 %
69400NaClpositivegrowth0-2.5 %

observation

@refobservation
67770quinones: MK-9(H6), MK-9(H4), MK-9(H8)
67771quinones: MK-9(H6)(61 %), MK-9(H4)(21%), MK-9(H8)(8%), MK-9(H2)(3%)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3044015963ribitol+carbon source
3044022599arabinose+carbon source
3044017057cellobiose+carbon source
3044023652dextrin+carbon source
3044028757fructose+carbon source
3044028260galactose+carbon source
3044017716lactose+carbon source
3044017306maltose+carbon source
3044029864mannitol+carbon source
3044028053melibiose+carbon source
3044017268myo-inositol+carbon source
3044026546rhamnose+carbon source
3044030911sorbitol+carbon source
3044030031succinate+carbon source
3044017992sucrose+carbon source
3044018222xylose+carbon source
3044017632nitrate+reduction
6940022599arabinose+growth
6940062968cellulose+/-growth
6940028757fructose+growth
6940017234glucose+growth
6940017268inositol+/-growth
6940037684mannose+/-growth
6940016634raffinose-growth
6940026546rhamnose+growth
6940017992sucrose+/-growth
6940018222xylose+growth
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
30440acid phosphatase+3.1.3.2
30440alkaline phosphatase+3.1.3.1
30440catalase+1.11.1.6
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase+3.1.3.1
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69400+--+--+-+-+/---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69400++/-+/--+++/--+++---+++/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17455soilCanakkale, GeliboluTurkeyTUR
67770SoilCanakkaleTurkeyTURAsia
67771From soilCanakkaleTurkeyTURAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

  • @ref: 17455
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17455
  • description: Actinomadura geliboluensis strain A8036 16S ribosomal RNA gene, partial sequence
  • accession: HQ157187
  • length: 1490
  • database: ena
  • NCBI tax ID: 882440

Genome sequences

  • @ref: 66792
  • description: Actinomadura geliboluensis A8036
  • accession: GCA_005889745
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 882440

GC content

@refGC-contentmethod
1745570.8fluorimetric
3044070.8
6777070.8thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno90.383no
flagellatedno97.585yes
gram-positiveyes88.257yes
anaerobicno97.936yes
aerobicyes86.722no
halophileno88.197no
spore-formingyes92.125yes
thermophileno96.154yes
glucose-utilyes88.14no
glucose-fermentno90.407yes

External links

@ref: 17455

culture collection no.: DSM 45508, KCTC 19868, JCM 19952

straininfo link

  • @ref: 86006
  • straininfo: 407716

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22021584Actinomadura geliboluensis sp. nov., isolated from soil.Sazak A, Camas M, Sproer C, Klenk HP, Sahin NInt J Syst Evol Microbiol10.1099/ijs.0.036145-02011Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Carbohydrates/analysis, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/analysis, *Soil Microbiology, TurkeyGenetics
Phylogeny32756615A sensitive pH indicator-based spectrophotometric assay for PHB depolymerase activity on microtiter plates.Camacho-Ruiz MA, Muller-Santos M, Hernandez-Mancillas XD, Armenta-Perez VP, Zamora-Gonzalez E, Rodriguez JAAnal Methods10.1039/d0ay00840k2020Amino Acid Sequence, Burkholderiaceae, Hydrogen-Ion Concentration, *Hydroxybutyrates, *Polyesters, RNA, Ribosomal, 16S, Streptomyces
Phylogeny34705623Actinomadura soli sp. nov., isolated from the top soil layer on basaltic material in Turkey.Saricaoglu S, Saygin H, Topkara AR, Gencbay T, Guven K, Cetin D, Sahin N, Isik KInt J Syst Evol Microbiol10.1099/ijsem.0.0050622021Actinomadura/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Turkey, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17455Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45508)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45508
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
30440Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2677628776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69400Wink, J.https://cdn.dsmz.de/wink/DSM%2045508.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
86006Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407716.1StrainInfo: A central database for resolving microbial strain identifiers